It's always seemed to me that a temporary solution would be to attach a metadata extension to either the beginning or end of an existing file type. If OSes recognized the fact then it wouldn't interfere with legacy programs not designed to read or understand said extension (in those circumstances the OS would only present a traditional file to a legacy program).
OSes that did not recognize the new type of file could install drivers that would enable them do so (a la installable file systems).
Metadata extensions on files could contain OS info (such as who created the file, or the name of the previous OS the file was installed on, its history of use, or version info, etc., etc.
Similarly, a section of the metadata space could be reserved only for program use, the same would go for the user. Moreover, one could envision a whole range of read, write, edit and erase permissions connected with any of this metadata.
There are many conceivable variations and I've been whingeing about the lack of any of them for decades. That said, any new system will likely be much better than the god-damn-awful antiquated system that we currently have now!
I think real file formats evolve into "boxes full of boxes".
For instance a DOCX file is really a ZIP file that has some XML files, PNG files and similar things in it. Similarly a PDF file is a composite object that has text, images, fonts, and similar things encoded inside it.
